website/full_javadoc/index-files/index-7.html

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  81 <A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
  82 <A NAME="_G_"><!-- --></A><H2>\r
  83 <B>G</B></H2>\r
  84 <DL>\r
  85 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#gapchar"><B>gapchar</B></A> - \r
  86 Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
  87 <DD>Dash char to be used as gap char in the alignments\r
  88 <DT><A HREF="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server"><B>GenericMetadataService</B></A>&lt;<A HREF="../compbio/ws/server/GenericMetadataService.html" title="type parameter in GenericMetadataService">T</A>&gt; - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/engine/PulledFileCache.html#get(java.lang.String)"><B>get(String)</B></A> - \r
  89 Static method in class compbio.engine.<A HREF="../compbio/engine/PulledFileCache.html" title="class in compbio.engine">PulledFileCache</A>\r
  90 <DD>&nbsp;\r
  91 <DT><A HREF="../compbio/stat/servlet/util/Totals.html#getAbandoned()"><B>getAbandoned()</B></A> - \r
  92 Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</A>\r
  93 <DD>&nbsp;\r
  94 <DT><A HREF="../compbio/stat/collector/StatDB.html#getAbandonedCount(java.sql.Timestamp, java.sql.Timestamp)"><B>getAbandonedCount(Timestamp, Timestamp)</B></A> - \r
  95 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</A>\r
  96 <DD>&nbsp;\r
  97 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#getAbandonedJobs()"><B>getAbandonedJobs()</B></A> - \r
  98 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
  99 <DD>Not collected.\r
 100 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getActualNumberofSequences()"><B>getActualNumberofSequences()</B></A> - \r
 101 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
 102 <DD>&nbsp;\r
 103 <DT><A HREF="../compbio/metadata/LimitExceededException.html#getActualNumberofSequences()"><B>getActualNumberofSequences()</B></A> - \r
 104 Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
 105 <DD>&nbsp;\r
 106 <DT><A HREF="../compbio/runner/OptionCombinator.html#getAllConstrainedParametersWithBorderValues(boolean)"><B>getAllConstrainedParametersWithBorderValues(boolean)</B></A> - \r
 107 Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
 108 <DD>&nbsp;\r
 109 <DT><A HREF="../compbio/runner/OptionCombinator.html#getAllConstrainedParametersWithRandomValues()"><B>getAllConstrainedParametersWithRandomValues()</B></A> - \r
 110 Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
 111 <DD>&nbsp;\r
 112 <DT><A HREF="../compbio/runner/OptionCombinator.html#getAllOptions()"><B>getAllOptions()</B></A> - \r
 113 Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
 114 <DD>&nbsp;\r
 115 <DT><A HREF="../compbio/runner/OptionCombinator.html#getAllParameters()"><B>getAllParameters()</B></A> - \r
 116 Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
 117 <DD>&nbsp;\r
 118 <DT><A HREF="../compbio/stat/servlet/util/StatCollection.html#getAllStat()"><B>getAllStat()</B></A> - \r
 119 Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</A>\r
 120 <DD>&nbsp;\r
 121 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getAllStats()"><B>getAllStats()</B></A> - \r
 122 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 123 <DD>&nbsp;\r
 124 <DT><A HREF="../compbio/data/msa/jaxws/GetAnnotation.html" title="class in compbio.data.msa.jaxws"><B>GetAnnotation</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetAnnotation.html#GetAnnotation()"><B>GetAnnotation()</B></A> - \r
 125 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetAnnotation.html" title="class in compbio.data.msa.jaxws">GetAnnotation</A>\r
 126 <DD>&nbsp;\r
 127 <DT><A HREF="../compbio/data/msa/SequenceAnnotation.html#getAnnotation(java.lang.String)"><B>getAnnotation(String)</B></A> - \r
 128 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A>\r
 129 <DD>Return the result of the job.\r
 130 <DT><A HREF="../compbio/ws/server/SequenceAnnotationService.html#getAnnotation(java.lang.String)"><B>getAnnotation(String)</B></A> - \r
 131 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/SequenceAnnotationService.html" title="class in compbio.ws.server">SequenceAnnotationService</A>\r
 132 <DD>&nbsp;\r
 133 <DT><A HREF="../compbio/ws/server/WSUtil.html#getAnnotation(java.lang.String, org.apache.log4j.Logger)"><B>getAnnotation(String, Logger)</B></A> - \r
 134 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
 135 <DD>&nbsp;\r
 136 <DT><A HREF="../compbio/data/sequence/ScoreManager.html#getAnnotationForSequence(java.lang.String)"><B>getAnnotationForSequence(String)</B></A> - \r
 137 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>\r
 138 <DD>&nbsp;\r
 139 <DT><A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html" title="class in compbio.data.msa.jaxws"><B>GetAnnotationResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html#GetAnnotationResponse()"><B>GetAnnotationResponse()</B></A> - \r
 140 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html" title="class in compbio.data.msa.jaxws">GetAnnotationResponse</A>\r
 141 <DD>&nbsp;\r
 142 <DT><A HREF="../compbio/runner/_NativeSpecHelper.html#getApproprieteQueue()"><B>getApproprieteQueue()</B></A> - \r
 143 Method in class compbio.runner.<A HREF="../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>\r
 144 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 145 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTested.html#getArg0()"><B>getArg0()</B></A> - \r
 146 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTested.html" title="class in compbio.data.msa.jaxws">GetLastTested</A>\r
 147 <DD>&nbsp;\r
 148 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html#getArg0()"><B>getArg0()</B></A> - \r
 149 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html" title="class in compbio.data.msa.jaxws">GetLastTestedOn</A>\r
 150 <DD>&nbsp;\r
 151 <DT><A HREF="../compbio/data/msa/jaxws/IsOperating.html#getArg0()"><B>getArg0()</B></A> - \r
 152 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/IsOperating.html" title="class in compbio.data.msa.jaxws">IsOperating</A>\r
 153 <DD>&nbsp;\r
 154 <DT><A HREF="../compbio/data/msa/jaxws/TestService.html#getArg0()"><B>getArg0()</B></A> - \r
 155 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestService.html" title="class in compbio.data.msa.jaxws">TestService</A>\r
 156 <DD>&nbsp;\r
 157 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)"><B>getArgument(String)</B></A> - \r
 158 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 159 <DD>Returns the argument by its name if found, NULL otherwise.\r
 160 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)"><B>getArgumentByOptionName(String)</B></A> - \r
 161 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 162 <DD>Returns the argument by option name, NULL if the argument is not found\r
 163 <DT><A HREF="../compbio/metadata/Preset.html#getArguments(compbio.metadata.RunnerConfig)"><B>getArguments(RunnerConfig&lt;T&gt;)</B></A> - \r
 164 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
 165 <DD>Converts list of options as String to type Option\r
 166 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getArguments()"><B>getArguments()</B></A> - \r
 167 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 168 <DD>Returns list of <A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> and <A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> supported by current
 169  runner\r
 170 <DT><A HREF="../compbio/engine/Configurator.html#getAsyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)"><B>getAsyncEngine(ConfiguredExecutable&lt;?&gt;, Executable.ExecProvider)</B></A> - \r
 171 Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
 172 <DD>&nbsp;\r
 173 <DT><A HREF="../compbio/engine/Configurator.html#getAsyncEngine(compbio.engine.client.ConfiguredExecutable)"><B>getAsyncEngine(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
 174 Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
 175 <DD>&nbsp;\r
 176 <DT><A HREF="../compbio/engine/Configurator.html#getAsyncEngine(java.lang.String)"><B>getAsyncEngine(String)</B></A> - \r
 177 Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
 178 <DD>&nbsp;\r
 179 <DT><A HREF="../compbio/metadata/Limit.html#getAvgSeqLength()"><B>getAvgSeqLength()</B></A> - \r
 180 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
 181 <DD>&nbsp;\r
 182 <DT><A HREF="../compbio/metadata/Limit.html#getAvgSequenceLength(java.util.List)"><B>getAvgSequenceLength(List&lt;FastaSequence&gt;)</B></A> - \r
 183 Static method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
 184 <DD>Calculates an average sequence length of the dataset\r
 185 <DT><A HREF="../compbio/runner/_impl/Runners.html#getBlastAllRunnable(java.lang.String)"><B>getBlastAllRunnable(String)</B></A> - \r
 186 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
 187 <DD>&nbsp;\r
 188 <DT><A HREF="../compbio/runner/_impl/Environment.html#getBlastBinDir()"><B>getBlastBinDir()</B></A> - \r
 189 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl">Environment</A>\r
 190 <DD>&nbsp;\r
 191 <DT><A HREF="../compbio/runner/_impl/Environment.html#getBlastDatabasesDir()"><B>getBlastDatabasesDir()</B></A> - \r
 192 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl">Environment</A>\r
 193 <DD>&nbsp;\r
 194 <DT><A HREF="../compbio/engine/Job.html#getByJobId(java.lang.String, java.util.List)"><B>getByJobId(String, List&lt;Job&gt;)</B></A> - \r
 195 Static method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
 196 <DD>&nbsp;\r
 197 <DT><A HREF="../compbio/engine/Job.html#getByTaskId(java.lang.String, java.util.List)"><B>getByTaskId(String, List&lt;Job&gt;)</B></A> - \r
 198 Static method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
 199 <DD>&nbsp;\r
 200 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getCalculationTime()"><B>getCalculationTime()</B></A> - \r
 201 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 202 <DD>&nbsp;\r
 203 <DT><A HREF="../compbio/stat/servlet/util/Totals.html#getCancelled()"><B>getCancelled()</B></A> - \r
 204 Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</A>\r
 205 <DD>&nbsp;\r
 206 <DT><A HREF="../compbio/stat/collector/StatDB.html#getCancelledCount(java.sql.Timestamp, java.sql.Timestamp)"><B>getCancelledCount(Timestamp, Timestamp)</B></A> - \r
 207 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</A>\r
 208 <DD>&nbsp;\r
 209 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#getCancelledJobs()"><B>getCancelledJobs()</B></A> - \r
 210 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
 211 <DD>&nbsp;\r
 212 <DT><A HREF="../compbio/metadata/ChunkHolder.html#getChunk()"><B>getChunk()</B></A> - \r
 213 Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
 214 <DD>&nbsp;\r
 215 <DT><A HREF="../compbio/engine/conf/DirectoryManager.html#getClass(java.lang.String)"><B>getClass(String)</B></A> - \r
 216 Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf">DirectoryManager</A>\r
 217 <DD>&nbsp;\r
 218 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getClusterCpuNum(java.lang.Class)"><B>getClusterCpuNum(Class&lt;? extends Executable&lt;?&gt;&gt;)</B></A> - \r
 219 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 220 <DD>&nbsp;\r
 221 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#getClusterJobId(java.lang.String)"><B>getClusterJobId(String)</B></A> - \r
 222 Static method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
 223 <DD>&nbsp;\r
 224 <DT><A HREF="../compbio/stat/collector/JobStat.html#getClusterJobId()"><B>getClusterJobId()</B></A> - \r
 225 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
 226 <DD>&nbsp;\r
 227 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#getClusterJobs()"><B>getClusterJobs()</B></A> - \r
 228 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
 229 <DD>&nbsp;\r
 230 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getClusterJobSettings()"><B>getClusterJobSettings()</B></A> - \r
 231 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 232 <DD>&nbsp;\r
 233 <DT><A HREF="../compbio/engine/client/Executable.html#getClusterJobSettings()"><B>getClusterJobSettings()</B></A> - \r
 234 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
 235 <DD>&nbsp;\r
 236 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getClusterJobSettings()"><B>getClusterJobSettings()</B></A> - \r
 237 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 238 <DD>&nbsp;\r
 239 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getClusterJobSettings()"><B>getClusterJobSettings()</B></A> - \r
 240 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
 241 <DD>&nbsp;\r
 242 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getClusterJobSettings()"><B>getClusterJobSettings()</B></A> - \r
 243 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 244 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 245 <DT><A HREF="../compbio/stat/servlet/util/StatCollection.html#getClusterStat()"><B>getClusterStat()</B></A> - \r
 246 Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</A>\r
 247 <DD>&nbsp;\r
 248 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
 249 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 250 <DD>&nbsp;\r
 251 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
 252 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
 253 <DD>&nbsp;\r
 254 <DT><A HREF="../compbio/engine/client/Util.html#getCommand(compbio.engine.client.Executable.ExecProvider, java.lang.Class)"><B>getCommand(Executable.ExecProvider, Class&lt;?&gt;)</B></A> - \r
 255 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 256 <DD>&nbsp;\r
 257 <DT><A HREF="../compbio/runner/_impl/BlastAll.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
 258 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>\r
 259 <DD>&nbsp;\r
 260 <DT><A HREF="../compbio/runner/_impl/Mcl.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
 261 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
 262 <DD>&nbsp;\r
 263 <DT><A HREF="../compbio/runner/_impl/PSIBlast.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
 264 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>\r
 265 <DD>&nbsp;\r
 266 <DT><A HREF="../compbio/runner/_impl/Ronn.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
 267 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>\r
 268 <DD>&nbsp;\r
 269 <DT><A HREF="../compbio/runner/_impl/RPSBlast.html#getCommand(compbio.engine.client.Executable.ExecProvider)"><B>getCommand(Executable.ExecProvider)</B></A> - \r
 270 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>\r
 271 <DD>&nbsp;\r
 272 <DT><A HREF="../compbio/runner/_impl/BlastAll.html#getCommandName()"><B>getCommandName()</B></A> - \r
 273 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>\r
 274 <DD>&nbsp;\r
 275 <DT><A HREF="../compbio/runner/_impl/Mcl.html#getCommandName()"><B>getCommandName()</B></A> - \r
 276 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
 277 <DD>&nbsp;\r
 278 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getCommandName()"><B>getCommandName()</B></A> - \r
 279 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
 280 <DD>&nbsp;\r
 281 <DT><A HREF="../compbio/runner/_impl/PSIBlast.html#getCommandName()"><B>getCommandName()</B></A> - \r
 282 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>\r
 283 <DD>&nbsp;\r
 284 <DT><A HREF="../compbio/runner/_impl/Ronn.html#getCommandName()"><B>getCommandName()</B></A> - \r
 285 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>\r
 286 <DD>&nbsp;\r
 287 <DT><A HREF="../compbio/runner/_impl/RPSBlast.html#getCommandName()"><B>getCommandName()</B></A> - \r
 288 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>\r
 289 <DD>&nbsp;\r
 290 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#getCommands()"><B>getCommands()</B></A> - \r
 291 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 292 <DD>&nbsp;\r
 293 <DT><A HREF="../compbio/ws/server/WSUtil.html#getCommands(java.util.List, java.lang.String)"><B>getCommands(List&lt;Option&lt;T&gt;&gt;, String)</B></A> - \r
 294 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
 295 <DD>&nbsp;\r
 296 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#getCommandString()"><B>getCommandString()</B></A> - \r
 297 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 298 <DD>&nbsp;\r
 299 <DT><A HREF="../compbio/engine/Job.html#getConfExecutable()"><B>getConfExecutable()</B></A> - \r
 300 Method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
 301 <DD>&nbsp;\r
 302 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getCPUTimeStat()"><B>getCPUTimeStat()</B></A> - \r
 303 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 304 <DD>&nbsp;\r
 305 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getCPUUsageTime()"><B>getCPUUsageTime()</B></A> - \r
 306 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 307 <DD>&nbsp;\r
 308 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 309 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 310 <DD>&nbsp;\r
 311 <DT><A HREF="../compbio/engine/client/Executable.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 312 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
 313 <DD><B>Deprecated.</B>&nbsp;\r
 314 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 315 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 316 <DD>This method cannot really tell whether the files has actually been
 317  created or not.\r
 318 <DT><A HREF="../compbio/runner/_impl/BlastAll.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 319 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>\r
 320 <DD>&nbsp;\r
 321 <DT><A HREF="../compbio/runner/_impl/Mcl.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 322 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
 323 <DD>&nbsp;\r
 324 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 325 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
 326 <DD>&nbsp;\r
 327 <DT><A HREF="../compbio/runner/_impl/OB.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 328 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>\r
 329 <DD>&nbsp;\r
 330 <DT><A HREF="../compbio/runner/_impl/PSIBlast.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 331 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>\r
 332 <DD>&nbsp;\r
 333 <DT><A HREF="../compbio/runner/_impl/Ronn.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 334 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>\r
 335 <DD>&nbsp;\r
 336 <DT><A HREF="../compbio/runner/_impl/RPSBlast.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 337 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>\r
 338 <DD>&nbsp;\r
 339 <DT><A HREF="../compbio/runner/conservation/AACon.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 340 Method in class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>\r
 341 <DD>&nbsp;\r
 342 <DT><A HREF="../compbio/runner/disorder/Jronn.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 343 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>\r
 344 <DD>&nbsp;\r
 345 <DT><A HREF="../compbio/runner/msa/ClustalW.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 346 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
 347 <DD>&nbsp;\r
 348 <DT><A HREF="../compbio/runner/msa/Muscle.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 349 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
 350 <DD>&nbsp;\r
 351 <DT><A HREF="../compbio/runner/msa/Probcons.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 352 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>\r
 353 <DD>&nbsp;\r
 354 <DT><A HREF="../compbio/runner/msa/Tcoffee.html#getCreatedFiles()"><B>getCreatedFiles()</B></A> - \r
 355 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
 356 <DD>&nbsp;\r
 357 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getDataTransfered()"><B>getDataTransfered()</B></A> - \r
 358 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 359 <DD>&nbsp;\r
 360 <DT><A HREF="../compbio/metadata/LimitsManager.html#getDefaultLimit()"><B>getDefaultLimit()</B></A> - \r
 361 Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
 362 <DD>&nbsp;\r
 363 <DT><A HREF="../compbio/metadata/Argument.html#getDefaultValue()"><B>getDefaultValue()</B></A> - \r
 364 Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
 365 <DD>&nbsp;\r
 366 <DT><A HREF="../compbio/metadata/Option.html#getDefaultValue()"><B>getDefaultValue()</B></A> - \r
 367 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 368 <DD>A default value of the option.\r
 369 <DT><A HREF="../compbio/engine/FilePuller.html#getDelay(java.util.concurrent.TimeUnit)"><B>getDelay(TimeUnit)</B></A> - \r
 370 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
 371 <DD>&nbsp;\r
 372 <DT><A HREF="../compbio/metadata/Argument.html#getDescription()"><B>getDescription()</B></A> - \r
 373 Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
 374 <DD>&nbsp;\r
 375 <DT><A HREF="../compbio/metadata/Option.html#getDescription()"><B>getDescription()</B></A> - \r
 376 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 377 <DD>A long description of the Option\r
 378 <DT><A HREF="../compbio/metadata/Preset.html#getDescription()"><B>getDescription()</B></A> - \r
 379 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
 380 <DD>&nbsp;\r
 381 <DT><A HREF="../compbio/stat/collector/StatDB.html#getEarliestRecord()"><B>getEarliestRecord()</B></A> - \r
 382 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</A>\r
 383 <DD>&nbsp;\r
 384 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getEmail()"><B>getEmail()</B></A> - \r
 385 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 386 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 387 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getEndTime()"><B>getEndTime()</B></A> - \r
 388 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 389 <DD>&nbsp;\r
 390 <DT><A HREF="../compbio/engine/LoadBalancer.html#getEngine(compbio.engine.client.Executable)"><B>getEngine(Executable&lt;?&gt;)</B></A> - \r
 391 Static method in class compbio.engine.<A HREF="../compbio/engine/LoadBalancer.html" title="class in compbio.engine">LoadBalancer</A>\r
 392 <DD>&nbsp;\r
 393 <DT><A HREF="../compbio/engine/LoadBalancer.html#getEngine(compbio.engine.client.Executable, java.util.List)"><B>getEngine(Executable&lt;V&gt;, List&lt;FastaSequence&gt;)</B></A> - \r
 394 Static method in class compbio.engine.<A HREF="../compbio/engine/LoadBalancer.html" title="class in compbio.engine">LoadBalancer</A>\r
 395 <DD>&nbsp;\r
 396 <DT><A HREF="../compbio/ws/server/WSUtil.html#getEngine(compbio.engine.client.ConfiguredExecutable)"><B>getEngine(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
 397 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
 398 <DD>&nbsp;\r
 399 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getEnvironment()"><B>getEnvironment()</B></A> - \r
 400 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 401 <DD>&nbsp;\r
 402 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getEnvironment()"><B>getEnvironment()</B></A> - \r
 403 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
 404 <DD>&nbsp;\r
 405 <DT><A HREF="../compbio/engine/client/EnvVariableProcessor.html#getEnvVariables(java.lang.String, java.lang.Class)"><B>getEnvVariables(String, Class&lt;?&gt;)</B></A> - \r
 406 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</A>\r
 407 <DD>&nbsp;\r
 408 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getError()"><B>getError()</B></A> - \r
 409 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 410 <DD>&nbsp;\r
 411 <DT><A HREF="../compbio/engine/client/Executable.html#getError()"><B>getError()</B></A> - \r
 412 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
 413 <DD>&nbsp;\r
 414 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#getError()"><B>getError()</B></A> - \r
 415 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 416 <DD>&nbsp;\r
 417 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getError()"><B>getError()</B></A> - \r
 418 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 419 <DD>&nbsp;\r
 420 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getError()"><B>getError()</B></A> - \r
 421 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
 422 <DD>&nbsp;\r
 423 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getError()"><B>getError()</B></A> - \r
 424 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 425 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 426 <DT><A HREF="../compbio/stat/collector/JobStat.html#getEscJobname()"><B>getEscJobname()</B></A> - \r
 427 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
 428 <DD>&nbsp;\r
 429 <DT><A HREF="../compbio/engine/client/Util.html#getExecProperty(java.lang.String, compbio.engine.client.Executable)"><B>getExecProperty(String, Executable&lt;?&gt;)</B></A> - \r
 430 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 431 <DD>&nbsp;\r
 432 <DT><A HREF="../compbio/engine/client/Util.html#getExecProperty(java.lang.String, java.lang.Class)"><B>getExecProperty(String, Class&lt;?&gt;)</B></A> - \r
 433 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 434 <DD>&nbsp;\r
 435 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getExecProvider()"><B>getExecProvider()</B></A> - \r
 436 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 437 <DD>&nbsp;\r
 438 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getExecProvider()"><B>getExecProvider()</B></A> - \r
 439 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
 440 <DD>&nbsp;\r
 441 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getExecutable()"><B>getExecutable()</B></A> - \r
 442 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 443 <DD>&nbsp;\r
 444 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getExecutable()"><B>getExecutable()</B></A> - \r
 445 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
 446 <DD>&nbsp;\r
 447 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getExecutionStat()"><B>getExecutionStat()</B></A> - \r
 448 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 449 <DD>&nbsp;\r
 450 <DT><A HREF="../compbio/engine/local/LocalExecutorService.html#getExecutor()"><B>getExecutor()</B></A> - \r
 451 Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalExecutorService.html" title="class in compbio.engine.local">LocalExecutorService</A>\r
 452 <DD>This method returns the single instance of CachedThreadPoolExecutor which
 453  it cashes internally\r
 454 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getExitStatus()"><B>getExitStatus()</B></A> - \r
 455 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 456 <DD>&nbsp;\r
 457 <DT><A HREF="../compbio/stat/servlet/util/Totals.html#getFailed()"><B>getFailed()</B></A> - \r
 458 Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</A>\r
 459 <DD>&nbsp;\r
 460 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#getFailedJobs()"><B>getFailedJobs()</B></A> - \r
 461 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
 462 <DD>Started & finished but did not produce result\r
 463 <DT><A HREF="../compbio/data/msa/jaxws/Align.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
 464 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws">Align</A>\r
 465 <DD>&nbsp;\r
 466 <DT><A HREF="../compbio/data/msa/jaxws/Analize.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
 467 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/Analize.html" title="class in compbio.data.msa.jaxws">Analize</A>\r
 468 <DD>&nbsp;\r
 469 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
 470 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</A>\r
 471 <DD>&nbsp;\r
 472 <DT><A HREF="../compbio/data/msa/jaxws/CustomAnalize.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
 473 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws">CustomAnalize</A>\r
 474 <DD>&nbsp;\r
 475 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
 476 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</A>\r
 477 <DD>&nbsp;\r
 478 <DT><A HREF="../compbio/data/msa/jaxws/PresetAnalize.html#getFastaSequences()"><B>getFastaSequences()</B></A> - \r
 479 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws">PresetAnalize</A>\r
 480 <DD>&nbsp;\r
 481 <DT><A HREF="../compbio/engine/FilePuller.html#getFile()"><B>getFile()</B></A> - \r
 482 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
 483 <DD>&nbsp;\r
 484 <DT><A HREF="../compbio/stat/collector/JobStat.html#getFinish()"><B>getFinish()</B></A> - \r
 485 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
 486 <DD>&nbsp;\r
 487 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#getFormatedSequence(int)"><B>getFormatedSequence(int)</B></A> - \r
 488 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
 489 <DD>Format sequence per width letter in one string.\r
 490 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#getFormattedFasta()"><B>getFormattedFasta()</B></A> - \r
 491 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
 492 <DD>&nbsp;\r
 493 <DT><A HREF="../compbio/engine/client/Util.html#getFullPath(java.lang.String, java.lang.String)"><B>getFullPath(String, String)</B></A> - \r
 494 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 495 <DD>&nbsp;\r
 496 <DT><A HREF="../compbio/metadata/Argument.html#getFurtherDetails()"><B>getFurtherDetails()</B></A> - \r
 497 Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
 498 <DD>&nbsp;\r
 499 <DT><A HREF="../compbio/metadata/Option.html#getFurtherDetails()"><B>getFurtherDetails()</B></A> - \r
 500 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 501 <DD>The URL where further details about the option can be found\r
 502 <DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#getGapchar()"><B>getGapchar()</B></A> - \r
 503 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
 504 <DD>&nbsp;\r
 505 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#getId()"><B>getId()</B></A> - \r
 506 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
 507 <DD>Gets the value of id\r
 508 <DT><A HREF="../compbio/stat/servlet/util/Totals.html#getIncomplete()"><B>getIncomplete()</B></A> - \r
 509 Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</A>\r
 510 <DD>&nbsp;\r
 511 <DT><A HREF="../compbio/stat/collector/StatDB.html#getIncompleteCount(java.sql.Timestamp, java.sql.Timestamp)"><B>getIncompleteCount(Timestamp, Timestamp)</B></A> - \r
 512 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</A>\r
 513 <DD>&nbsp;\r
 514 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#getIncompleteJobs()"><B>getIncompleteJobs()</B></A> - \r
 515 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
 516 <DD>&nbsp;\r
 517 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getInput()"><B>getInput()</B></A> - \r
 518 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 519 <DD>Not all input paths are relative! Input path could be absolute!\r
 520 <DT><A HREF="../compbio/engine/client/Executable.html#getInput()"><B>getInput()</B></A> - \r
 521 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
 522 <DD>&nbsp;\r
 523 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#getInput()"><B>getInput()</B></A> - \r
 524 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 525 <DD>&nbsp;\r
 526 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getInput()"><B>getInput()</B></A> - \r
 527 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 528 <DD>&nbsp;\r
 529 <DT><A HREF="../compbio/runner/_impl/BlastAll.html#getInput()"><B>getInput()</B></A> - \r
 530 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>\r
 531 <DD>&nbsp;\r
 532 <DT><A HREF="../compbio/runner/_impl/Mcl.html#getInput()"><B>getInput()</B></A> - \r
 533 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
 534 <DD>&nbsp;\r
 535 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getInput()"><B>getInput()</B></A> - \r
 536 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
 537 <DD>&nbsp;\r
 538 <DT><A HREF="../compbio/runner/_impl/OB.html#getInput()"><B>getInput()</B></A> - \r
 539 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>\r
 540 <DD>&nbsp;\r
 541 <DT><A HREF="../compbio/runner/_impl/PSIBlast.html#getInput()"><B>getInput()</B></A> - \r
 542 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>\r
 543 <DD>&nbsp;\r
 544 <DT><A HREF="../compbio/runner/_impl/Ronn.html#getInput()"><B>getInput()</B></A> - \r
 545 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>\r
 546 <DD>&nbsp;\r
 547 <DT><A HREF="../compbio/runner/_impl/RPSBlast.html#getInput()"><B>getInput()</B></A> - \r
 548 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>\r
 549 <DD>&nbsp;\r
 550 <DT><A HREF="../compbio/stat/collector/JobStat.html#getInputSize()"><B>getInputSize()</B></A> - \r
 551 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
 552 <DD>&nbsp;\r
 553 <DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#getInstance(compbio.engine.client.ConfiguredExecutable)"><B>getInstance(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
 554 Static method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>\r
 555 <DD>&nbsp;\r
 556 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getIOWait()"><B>getIOWait()</B></A> - \r
 557 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 558 <DD>&nbsp;\r
 559 <DT><A HREF="../compbio/stat/collector/JobStat.html#getIsCancelled()"><B>getIsCancelled()</B></A> - \r
 560 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
 561 <DD>&nbsp;\r
 562 <DT><A HREF="../compbio/stat/collector/JobStat.html#getIsCollected()"><B>getIsCollected()</B></A> - \r
 563 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
 564 <DD>&nbsp;\r
 565 <DT><A HREF="../compbio/stat/collector/JobStat.html#getIsFinished()"><B>getIsFinished()</B></A> - \r
 566 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
 567 <DD>&nbsp;\r
 568 <DT><A HREF="../compbio/engine/client/Util.html#getJava()"><B>getJava()</B></A> - \r
 569 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 570 <DD>Returns the absolute path to the Java executable from JAVA_HOME\r
 571 <DT><A HREF="../compbio/data/msa/jaxws/CancelJob.html#getJobId()"><B>getJobId()</B></A> - \r
 572 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CancelJob.html" title="class in compbio.data.msa.jaxws">CancelJob</A>\r
 573 <DD>&nbsp;\r
 574 <DT><A HREF="../compbio/data/msa/jaxws/GetAnnotation.html#getJobId()"><B>getJobId()</B></A> - \r
 575 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetAnnotation.html" title="class in compbio.data.msa.jaxws">GetAnnotation</A>\r
 576 <DD>&nbsp;\r
 577 <DT><A HREF="../compbio/data/msa/jaxws/GetJobStatus.html#getJobId()"><B>getJobId()</B></A> - \r
 578 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws">GetJobStatus</A>\r
 579 <DD>&nbsp;\r
 580 <DT><A HREF="../compbio/data/msa/jaxws/GetResult.html#getJobId()"><B>getJobId()</B></A> - \r
 581 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws">GetResult</A>\r
 582 <DD>&nbsp;\r
 583 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#getJobId()"><B>getJobId()</B></A> - \r
 584 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</A>\r
 585 <DD>&nbsp;\r
 586 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getJobId()"><B>getJobId()</B></A> - \r
 587 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 588 <DD>&nbsp;\r
 589 <DT><A HREF="../compbio/engine/ClusterJobId.html#getJobId()"><B>getJobId()</B></A> - \r
 590 Method in class compbio.engine.<A HREF="../compbio/engine/ClusterJobId.html" title="class in compbio.engine">ClusterJobId</A>\r
 591 <DD>&nbsp;\r
 592 <DT><A HREF="../compbio/engine/Job.html#getJobId()"><B>getJobId()</B></A> - \r
 593 Method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
 594 <DD>&nbsp;\r
 595 <DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#getJobInfo()"><B>getJobInfo()</B></A> - \r
 596 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>\r
 597 <DD>This method will block before the calculation has completed and then
 598  return the object containing a job execution statistics\r
 599 <DT><A HREF="../compbio/stat/collector/JobStat.html#getJobname()"><B>getJobname()</B></A> - \r
 600 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
 601 <DD>&nbsp;\r
 602 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#getJobNumber()"><B>getJobNumber()</B></A> - \r
 603 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
 604 <DD>&nbsp;\r
 605 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getJobPriority()"><B>getJobPriority()</B></A> - \r
 606 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 607 <DD>&nbsp;\r
 608 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#getJobs()"><B>getJobs()</B></A> - \r
 609 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
 610 <DD>&nbsp;\r
 611 <DT><A HREF="../compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws"><B>GetJobStatus</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetJobStatus.html#GetJobStatus()"><B>GetJobStatus()</B></A> - \r
 612 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatus.html" title="class in compbio.data.msa.jaxws">GetJobStatus</A>\r
 613 <DD>&nbsp;\r
 614 <DT><A HREF="../compbio/data/msa/JManagement.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 615 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>\r
 616 <DD>Return the status of the job.\r
 617 <DT><A HREF="../compbio/engine/AsyncExecutor.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 618 Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>\r
 619 <DD>Query the status of the job\r
 620 <DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 621 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>\r
 622 <DD>This will never return clust.engine.JobStatus.CANCELLED as for sun grid
 623  engine cancelled job is the same as failed.\r
 624 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#getJobStatus(compbio.engine.ClusterJobId)"><B>getJobStatus(ClusterJobId)</B></A> - \r
 625 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
 626 <DD>Apparently completed jobs cannot be found! If this happened most likely
 627  that the job is not running any more and Most likely it has been
 628  cancelled, finished or failed.\r
 629 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#getJobStatus(int)"><B>getJobStatus(int)</B></A> - \r
 630 Static method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
 631 <DD><B>Deprecated.</B>&nbsp;\r
 632 <DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#getJobStatus()"><B>getJobStatus()</B></A> - \r
 633 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>\r
 634 <DD>&nbsp;\r
 635 <DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 636 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
 637 <DD>&nbsp;\r
 638 <DT><A HREF="../compbio/engine/local/LocalEngineUtil.html#getJobStatus(java.util.concurrent.Future)"><B>getJobStatus(Future&lt;ConfiguredExecutable&lt;?&gt;&gt;)</B></A> - \r
 639 Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</A>\r
 640 <DD>&nbsp;\r
 641 <DT><A HREF="../compbio/engine/local/LocalRunner.html#getJobStatus()"><B>getJobStatus()</B></A> - \r
 642 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>\r
 643 <DD>&nbsp;\r
 644 <DT><A HREF="../compbio/engine/SyncExecutor.html#getJobStatus()"><B>getJobStatus()</B></A> - \r
 645 Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>\r
 646 <DD>Query the status of the job by its id.\r
 647 <DT><A HREF="../compbio/ws/server/ClustalOWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 648 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
 649 <DD>&nbsp;\r
 650 <DT><A HREF="../compbio/ws/server/ClustalWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 651 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
 652 <DD>&nbsp;\r
 653 <DT><A HREF="../compbio/ws/server/GenericMetadataService.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 654 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</A>\r
 655 <DD>&nbsp;\r
 656 <DT><A HREF="../compbio/ws/server/MafftWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 657 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
 658 <DD>&nbsp;\r
 659 <DT><A HREF="../compbio/ws/server/MuscleWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 660 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
 661 <DD>&nbsp;\r
 662 <DT><A HREF="../compbio/ws/server/ProbconsWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 663 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
 664 <DD>&nbsp;\r
 665 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 666 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
 667 <DD>&nbsp;\r
 668 <DT><A HREF="../compbio/ws/server/WSUtil.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
 669 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
 670 <DD>&nbsp;\r
 671 <DT><A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws"><B>GetJobStatusResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html#GetJobStatusResponse()"><B>GetJobStatusResponse()</B></A> - \r
 672 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws">GetJobStatusResponse</A>\r
 673 <DD>&nbsp;\r
 674 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTested.html" title="class in compbio.data.msa.jaxws"><B>GetLastTested</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLastTested.html#GetLastTested()"><B>GetLastTested()</B></A> - \r
 675 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTested.html" title="class in compbio.data.msa.jaxws">GetLastTested</A>\r
 676 <DD>&nbsp;\r
 677 <DT><A HREF="../compbio/data/msa/RegistryWS.html#getLastTested(compbio.ws.client.Services)"><B>getLastTested(Services)</B></A> - \r
 678 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>\r
 679 <DD>Number of seconds since the last test.\r
 680 <DT><A HREF="../compbio/ws/server/RegistryWS.html#getLastTested(compbio.ws.client.Services)"><B>getLastTested(Services)</B></A> - \r
 681 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</A>\r
 682 <DD>&nbsp;\r
 683 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html" title="class in compbio.data.msa.jaxws"><B>GetLastTestedOn</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html#GetLastTestedOn()"><B>GetLastTestedOn()</B></A> - \r
 684 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedOn.html" title="class in compbio.data.msa.jaxws">GetLastTestedOn</A>\r
 685 <DD>&nbsp;\r
 686 <DT><A HREF="../compbio/data/msa/RegistryWS.html#getLastTestedOn(compbio.ws.client.Services)"><B>getLastTestedOn(Services)</B></A> - \r
 687 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>\r
 688 <DD>The date and time the service has been verified to work last time\r
 689 <DT><A HREF="../compbio/ws/server/RegistryWS.html#getLastTestedOn(compbio.ws.client.Services)"><B>getLastTestedOn(Services)</B></A> - \r
 690 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</A>\r
 691 <DD>Can potentially return null if the service has not been tested yet.\r
 692 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html" title="class in compbio.data.msa.jaxws"><B>GetLastTestedOnResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html#GetLastTestedOnResponse()"><B>GetLastTestedOnResponse()</B></A> - \r
 693 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedOnResponse</A>\r
 694 <DD>&nbsp;\r
 695 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html" title="class in compbio.data.msa.jaxws"><B>GetLastTestedResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html#GetLastTestedResponse()"><B>GetLastTestedResponse()</B></A> - \r
 696 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedResponse</A>\r
 697 <DD>&nbsp;\r
 698 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#getLength()"><B>getLength()</B></A> - \r
 699 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
 700 <DD>&nbsp;\r
 701 <DT><A HREF="../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws"><B>GetLimit</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLimit.html#GetLimit()"><B>GetLimit()</B></A> - \r
 702 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws">GetLimit</A>\r
 703 <DD>&nbsp;\r
 704 <DT><A HREF="../compbio/data/msa/Metadata.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 705 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>\r
 706 <DD>Get a Limit for a preset.\r
 707 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 708 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 709 <DD>&nbsp;\r
 710 <DT><A HREF="../compbio/engine/client/Executable.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 711 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
 712 <DD>&nbsp;\r
 713 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 714 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 715 <DD>&nbsp;\r
 716 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 717 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
 718 <DD>&nbsp;\r
 719 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 720 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 721 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 722 <DT><A HREF="../compbio/ws/server/ClustalOWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 723 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
 724 <DD>&nbsp;\r
 725 <DT><A HREF="../compbio/ws/server/ClustalWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 726 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
 727 <DD>&nbsp;\r
 728 <DT><A HREF="../compbio/ws/server/GenericMetadataService.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 729 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</A>\r
 730 <DD>&nbsp;\r
 731 <DT><A HREF="../compbio/ws/server/MafftWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 732 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
 733 <DD>&nbsp;\r
 734 <DT><A HREF="../compbio/ws/server/MuscleWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 735 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
 736 <DD>&nbsp;\r
 737 <DT><A HREF="../compbio/ws/server/ProbconsWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 738 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
 739 <DD>&nbsp;\r
 740 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
 741 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
 742 <DD>&nbsp;\r
 743 <DT><A HREF="../compbio/metadata/LimitsManager.html#getLimitByName(java.lang.String)"><B>getLimitByName(String)</B></A> - \r
 744 Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
 745 <DD>&nbsp;\r
 746 <DT><A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws"><B>GetLimitResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html#GetLimitResponse()"><B>GetLimitResponse()</B></A> - \r
 747 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws">GetLimitResponse</A>\r
 748 <DD>&nbsp;\r
 749 <DT><A HREF="../compbio/data/msa/jaxws/GetLimits.html" title="class in compbio.data.msa.jaxws"><B>GetLimits</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLimits.html#GetLimits()"><B>GetLimits()</B></A> - \r
 750 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimits.html" title="class in compbio.data.msa.jaxws">GetLimits</A>\r
 751 <DD>&nbsp;\r
 752 <DT><A HREF="../compbio/data/msa/Metadata.html#getLimits()"><B>getLimits()</B></A> - \r
 753 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>\r
 754 <DD>List Limits supported by a web service.\r
 755 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getLimits()"><B>getLimits()</B></A> - \r
 756 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 757 <DD>&nbsp;\r
 758 <DT><A HREF="../compbio/engine/client/Executable.html#getLimits()"><B>getLimits()</B></A> - \r
 759 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
 760 <DD>&nbsp;\r
 761 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getLimits()"><B>getLimits()</B></A> - \r
 762 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 763 <DD>&nbsp;\r
 764 <DT><A HREF="../compbio/engine/client/Util.html#getLimits(java.lang.Class)"><B>getLimits(Class&lt;T&gt;)</B></A> - \r
 765 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 766 <DD>For now just assume that all parameters which came in needs setting it
 767  will be a client responsibility to prepare RunnerConfig object then\r
 768 <DT><A HREF="../compbio/metadata/LimitsManager.html#getLimits()"><B>getLimits()</B></A> - \r
 769 Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
 770 <DD>&nbsp;\r
 771 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getLimits()"><B>getLimits()</B></A> - \r
 772 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
 773 <DD>&nbsp;\r
 774 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getLimits()"><B>getLimits()</B></A> - \r
 775 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 776 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 777 <DT><A HREF="../compbio/ws/server/ClustalOWS.html#getLimits()"><B>getLimits()</B></A> - \r
 778 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
 779 <DD>&nbsp;\r
 780 <DT><A HREF="../compbio/ws/server/ClustalWS.html#getLimits()"><B>getLimits()</B></A> - \r
 781 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
 782 <DD>&nbsp;\r
 783 <DT><A HREF="../compbio/ws/server/GenericMetadataService.html#getLimits()"><B>getLimits()</B></A> - \r
 784 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</A>\r
 785 <DD>&nbsp;\r
 786 <DT><A HREF="../compbio/ws/server/MafftWS.html#getLimits()"><B>getLimits()</B></A> - \r
 787 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
 788 <DD>&nbsp;\r
 789 <DT><A HREF="../compbio/ws/server/MuscleWS.html#getLimits()"><B>getLimits()</B></A> - \r
 790 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
 791 <DD>&nbsp;\r
 792 <DT><A HREF="../compbio/ws/server/ProbconsWS.html#getLimits()"><B>getLimits()</B></A> - \r
 793 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
 794 <DD>&nbsp;\r
 795 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#getLimits()"><B>getLimits()</B></A> - \r
 796 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
 797 <DD>&nbsp;\r
 798 <DT><A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws"><B>GetLimitsResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html#GetLimitsResponse()"><B>GetLimitsResponse()</B></A> - \r
 799 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws">GetLimitsResponse</A>\r
 800 <DD>&nbsp;\r
 801 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#getLocalJobs()"><B>getLocalJobs()</B></A> - \r
 802 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
 803 <DD>&nbsp;\r
 804 <DT><A HREF="../compbio/engine/conf/PropertyHelperManager.html#getLocalPath()"><B>getLocalPath()</B></A> - \r
 805 Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</A>\r
 806 <DD>Method return the absolute path to the project root directory.\r
 807 <DT><A HREF="../compbio/stat/servlet/util/StatCollection.html#getLocalStat()"><B>getLocalStat()</B></A> - \r
 808 Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</A>\r
 809 <DD>&nbsp;\r
 810 <DT><A HREF="../compbio/metadata/ValueConstrain.html#getMax()"><B>getMax()</B></A> - \r
 811 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
 812 <DD>&nbsp;\r
 813 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getMaxVMem()"><B>getMaxVMem()</B></A> - \r
 814 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 815 <DD>&nbsp;\r
 816 <DT><A HREF="../compbio/runner/_impl/Runners.html#getMclRunnable(java.lang.String)"><B>getMclRunnable(String)</B></A> - \r
 817 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
 818 <DD>&nbsp;\r
 819 <DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#getMemoryLimit()"><B>getMemoryLimit()</B></A> - \r
 820 Method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
 821 <DD><B>Deprecated.</B>&nbsp;return max memory limit in Mb\r
 822 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getMemoryStat()"><B>getMemoryStat()</B></A> - \r
 823 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
 824 <DD>&nbsp;\r
 825 <DT><A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
 826 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/JobSubmissionExceptionBean.html" title="class in compbio.data.msa.jaxws">JobSubmissionExceptionBean</A>\r
 827 <DD>&nbsp;\r
 828 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
 829 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
 830 <DD>&nbsp;\r
 831 <DT><A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
 832 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws">ResultNotAvailableExceptionBean</A>\r
 833 <DD>&nbsp;\r
 834 <DT><A HREF="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
 835 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html" title="class in compbio.data.msa.jaxws">UnsupportedRuntimeExceptionBean</A>\r
 836 <DD>&nbsp;\r
 837 <DT><A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html#getMessage()"><B>getMessage()</B></A> - \r
 838 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html" title="class in compbio.data.msa.jaxws">WrongParameterExceptionBean</A>\r
 839 <DD>&nbsp;\r
 840 <DT><A HREF="../compbio/data/sequence/Alignment.html#getMetadata()"><B>getMetadata()</B></A> - \r
 841 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
 842 <DD>&nbsp;\r
 843 <DT><A HREF="../compbio/data/sequence/ConservationMethod.html#getMethod(java.lang.String)"><B>getMethod(String)</B></A> - \r
 844 Static method in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence">ConservationMethod</A>\r
 845 <DD>&nbsp;\r
 846 <DT><A HREF="../compbio/data/sequence/Score.html#getMethod()"><B>getMethod()</B></A> - \r
 847 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
 848 <DD>Returns the ConservationMethod\r
 849 <DT><A HREF="../compbio/metadata/ValueConstrain.html#getMin()"><B>getMin()</B></A> - \r
 850 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
 851 <DD>&nbsp;\r
 852 <DT><A HREF="../compbio/metadata/Argument.html#getName()"><B>getName()</B></A> - \r
 853 Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
 854 <DD>&nbsp;\r
 855 <DT><A HREF="../compbio/metadata/Option.html#getName()"><B>getName()</B></A> - \r
 856 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 857 <DD>Human readable name of the option\r
 858 <DT><A HREF="../compbio/metadata/Preset.html#getName()"><B>getName()</B></A> - \r
 859 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
 860 <DD>&nbsp;\r
 861 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getName()"><B>getName()</B></A> - \r
 862 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 863 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 864 <DT><A HREF="../compbio/runner/_NativeSpecHelper.html#getNativeSpec()"><B>getNativeSpec()</B></A> - \r
 865 Method in class compbio.runner.<A HREF="../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>\r
 866 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 867 <DT><A HREF="../compbio/runner/_impl/Runners.html#getNetNglycRunnable(java.lang.String)"><B>getNetNglycRunnable(String)</B></A> - \r
 868 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
 869 <DD>&nbsp;\r
 870 <DT><A HREF="../compbio/metadata/ChunkHolder.html#getNextPosition()"><B>getNextPosition()</B></A> - \r
 871 Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
 872 <DD>&nbsp;\r
 873 <DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#getNumberOfScores()"><B>getNumberOfScores()</B></A> - \r
 874 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>\r
 875 <DD>&nbsp;\r
 876 <DT><A HREF="../compbio/data/sequence/ScoreManager.html#getNumberOfSeq()"><B>getNumberOfSeq()</B></A> - \r
 877 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>\r
 878 <DD>&nbsp;\r
 879 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getNumberOfSequencesAllowed()"><B>getNumberOfSequencesAllowed()</B></A> - \r
 880 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
 881 <DD>&nbsp;\r
 882 <DT><A HREF="../compbio/metadata/LimitExceededException.html#getNumberOfSequencesAllowed()"><B>getNumberOfSequencesAllowed()</B></A> - \r
 883 Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
 884 <DD>&nbsp;\r
 885 <DT><A HREF="../compbio/runner/_impl/Runners.html#getOBRunnable(java.lang.String)"><B>getOBRunnable(String)</B></A> - \r
 886 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
 887 <DD>&nbsp;\r
 888 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#getOnelineFasta()"><B>getOnelineFasta()</B></A> - \r
 889 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
 890 <DD>&nbsp;\r
 891 <DT><A HREF="../compbio/metadata/Parameter.html#getOptionName()"><B>getOptionName()</B></A> - \r
 892 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
 893 <DD>&nbsp;\r
 894 <DT><A HREF="../compbio/metadata/Option.html#getOptionNames()"><B>getOptionNames()</B></A> - \r
 895 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 896 <DD>&nbsp;\r
 897 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlign.html#getOptions()"><B>getOptions()</B></A> - \r
 898 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlign.html" title="class in compbio.data.msa.jaxws">CustomAlign</A>\r
 899 <DD>&nbsp;\r
 900 <DT><A HREF="../compbio/data/msa/jaxws/CustomAnalize.html#getOptions()"><B>getOptions()</B></A> - \r
 901 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalize.html" title="class in compbio.data.msa.jaxws">CustomAnalize</A>\r
 902 <DD>&nbsp;\r
 903 <DT><A HREF="../compbio/metadata/Preset.html#getOptions()"><B>getOptions()</B></A> - \r
 904 Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
 905 <DD>&nbsp;\r
 906 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getOptions()"><B>getOptions()</B></A> - \r
 907 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 908 <DD>Returns the list of the Options supported by the executable of type T\r
 909 <DT><A HREF="../compbio/runner/OptionCombinator.html#getOptionsAtRandom()"><B>getOptionsAtRandom()</B></A> - \r
 910 Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
 911 <DD>&nbsp;\r
 912 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getOutput()"><B>getOutput()</B></A> - \r
 913 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 914 <DD>&nbsp;\r
 915 <DT><A HREF="../compbio/engine/client/Executable.html#getOutput()"><B>getOutput()</B></A> - \r
 916 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
 917 <DD>&nbsp;\r
 918 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#getOutput()"><B>getOutput()</B></A> - \r
 919 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 920 <DD>&nbsp;\r
 921 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getOutput()"><B>getOutput()</B></A> - \r
 922 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 923 <DD>&nbsp;\r
 924 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getOutput()"><B>getOutput()</B></A> - \r
 925 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
 926 <DD>&nbsp;\r
 927 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getOutput()"><B>getOutput()</B></A> - \r
 928 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 929 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 930 <DT><A HREF="../compbio/runner/disorder/IUPred.html#getOutput()"><B>getOutput()</B></A> - \r
 931 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>\r
 932 <DD>&nbsp;\r
 933 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getParameters()"><B>getParameters()</B></A> - \r
 934 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 935 <DD>&nbsp;\r
 936 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
 937 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
 938 <DD>&nbsp;\r
 939 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getParameters()"><B>getParameters()</B></A> - \r
 940 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
 941 <DD>&nbsp;\r
 942 <DT><A HREF="../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
 943 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
 944 <DD>&nbsp;\r
 945 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#getParameters()"><B>getParameters()</B></A> - \r
 946 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 947 <DD>&nbsp;\r
 948 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
 949 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
 950 <DD>&nbsp;\r
 951 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getParameters()"><B>getParameters()</B></A> - \r
 952 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 953 <DD>Returns the list of parameters supported executable of type T.\r
 954 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
 955 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
 956 <DD>&nbsp;\r
 957 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
 958 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
 959 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
 960 <DT><A HREF="../compbio/runner/conservation/AACon.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
 961 Method in class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>\r
 962 <DD>&nbsp;\r
 963 <DT><A HREF="../compbio/runner/disorder/Jronn.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
 964 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>\r
 965 <DD>&nbsp;\r
 966 <DT><A HREF="../compbio/runner/msa/ClustalO.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
 967 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>\r
 968 <DD>&nbsp;\r
 969 <DT><A HREF="../compbio/runner/msa/Tcoffee.html#getParameters(compbio.engine.client.Executable.ExecProvider)"><B>getParameters(Executable.ExecProvider)</B></A> - \r
 970 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
 971 <DD>&nbsp;\r
 972 <DT><A HREF="../compbio/engine/client/CommandBuilder.html#getParamValue(java.lang.String)"><B>getParamValue(String)</B></A> - \r
 973 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
 974 <DD>&nbsp;\r
 975 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html#getPosition()"><B>getPosition()</B></A> - \r
 976 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatistics.html" title="class in compbio.data.msa.jaxws">PullExecStatistics</A>\r
 977 <DD>&nbsp;\r
 978 <DT><A HREF="../compbio/metadata/Argument.html#getPossibleValues()"><B>getPossibleValues()</B></A> - \r
 979 Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
 980 <DD>&nbsp;\r
 981 <DT><A HREF="../compbio/metadata/Option.html#getPossibleValues()"><B>getPossibleValues()</B></A> - \r
 982 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 983 <DD>List of possible optionNames\r
 984 <DT><A HREF="../compbio/metadata/Parameter.html#getPossibleValues()"><B>getPossibleValues()</B></A> - \r
 985 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
 986 <DD>List is more convenient to work with\r
 987 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlign.html#getPreset()"><B>getPreset()</B></A> - \r
 988 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlign.html" title="class in compbio.data.msa.jaxws">PresetAlign</A>\r
 989 <DD>&nbsp;\r
 990 <DT><A HREF="../compbio/data/msa/jaxws/PresetAnalize.html#getPreset()"><B>getPreset()</B></A> - \r
 991 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalize.html" title="class in compbio.data.msa.jaxws">PresetAnalize</A>\r
 992 <DD>&nbsp;\r
 993 <DT><A HREF="../compbio/metadata/Limit.html#getPreset()"><B>getPreset()</B></A> - \r
 994 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
 995 <DD>&nbsp;\r
 996 <DT><A HREF="../compbio/metadata/PresetManager.html#getPresetByName(java.lang.String)"><B>getPresetByName(String)</B></A> - \r
 997 Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
 998 <DD>&nbsp;\r
 999 <DT><A HREF="../compbio/data/msa/jaxws/GetLimit.html#getPresetName()"><B>getPresetName()</B></A> - \r
1000 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimit.html" title="class in compbio.data.msa.jaxws">GetLimit</A>\r
1001 <DD>&nbsp;\r
1002 <DT><A HREF="../compbio/data/msa/jaxws/GetPresets.html" title="class in compbio.data.msa.jaxws"><B>GetPresets</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetPresets.html#GetPresets()"><B>GetPresets()</B></A> - \r
1003 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetPresets.html" title="class in compbio.data.msa.jaxws">GetPresets</A>\r
1004 <DD>&nbsp;\r
1005 <DT><A HREF="../compbio/data/msa/Metadata.html#getPresets()"><B>getPresets()</B></A> - \r
1006 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>\r
1007 <DD>Get presets supported by a web service\r
1008 <DT><A HREF="../compbio/metadata/PresetManager.html#getPresets()"><B>getPresets()</B></A> - \r
1009 Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
1010 <DD>&nbsp;\r
1011 <DT><A HREF="../compbio/runner/Util.html#getPresets(java.lang.Class)"><B>getPresets(Class&lt;? extends Executable&lt;T&gt;&gt;)</B></A> - \r
1012 Static method in class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>\r
1013 <DD>&nbsp;\r
1014 <DT><A HREF="../compbio/ws/server/ClustalOWS.html#getPresets()"><B>getPresets()</B></A> - \r
1015 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
1016 <DD>&nbsp;\r
1017 <DT><A HREF="../compbio/ws/server/ClustalWS.html#getPresets()"><B>getPresets()</B></A> - \r
1018 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
1019 <DD>&nbsp;\r
1020 <DT><A HREF="../compbio/ws/server/GenericMetadataService.html#getPresets()"><B>getPresets()</B></A> - \r
1021 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</A>\r
1022 <DD>&nbsp;\r
1023 <DT><A HREF="../compbio/ws/server/MafftWS.html#getPresets()"><B>getPresets()</B></A> - \r
1024 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
1025 <DD>&nbsp;\r
1026 <DT><A HREF="../compbio/ws/server/MuscleWS.html#getPresets()"><B>getPresets()</B></A> - \r
1027 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
1028 <DD>&nbsp;\r
1029 <DT><A HREF="../compbio/ws/server/ProbconsWS.html#getPresets()"><B>getPresets()</B></A> - \r
1030 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
1031 <DD>&nbsp;\r
1032 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#getPresets()"><B>getPresets()</B></A> - \r
1033 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
1034 <DD>&nbsp;\r
1035 <DT><A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws"><B>GetPresetsResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html#GetPresetsResponse()"><B>GetPresetsResponse()</B></A> - \r
1036 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws">GetPresetsResponse</A>\r
1037 <DD>&nbsp;\r
1038 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getPrmSeparator()"><B>getPrmSeparator()</B></A> - \r
1039 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
1040 <DD>&nbsp;\r
1041 <DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#getProgram()"><B>getProgram()</B></A> - \r
1042 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
1043 <DD>&nbsp;\r
1044 <DT><A HREF="../compbio/engine/FilePuller.html#getProgress()"><B>getProgress()</B></A> - \r
1045 Method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
1046 <DD>&nbsp;\r
1047 <DT><A HREF="../compbio/engine/ProgressGetter.html#getProgress(java.lang.String)"><B>getProgress(String)</B></A> - \r
1048 Static method in class compbio.engine.<A HREF="../compbio/engine/ProgressGetter.html" title="class in compbio.engine">ProgressGetter</A>\r
1049 <DD>&nbsp;\r
1050 <DT><A HREF="../compbio/ws/server/WSUtil.html#getProgress(java.lang.String)"><B>getProgress(String)</B></A> - \r
1051 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
1052 <DD>&nbsp;\r
1053 <DT><A HREF="../compbio/engine/conf/PropertyHelperManager.html#getPropertyHelper()"><B>getPropertyHelper()</B></A> - \r
1054 Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/PropertyHelperManager.html" title="class in compbio.engine.conf">PropertyHelperManager</A>\r
1055 <DD>Ways to fix path problem: 1) find a path to WEB-INF directory based on
1056  the path to a known class.\r
1057 <DT><A HREF="../compbio/runner/_impl/Runners.html#getPSIBlastRunnable(java.lang.String)"><B>getPSIBlastRunnable(String)</B></A> - \r
1058 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
1059 <DD>&nbsp;\r
1060 <DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#getQueue(int, int)"><B>getQueue(int, int)</B></A> - \r
1061 Static method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
1062 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
1063 <DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#getQueue(java.lang.String)"><B>getQueue(String)</B></A> - \r
1064 Method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
1065 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
1066 <DT><A HREF="../compbio/runner/_NativeSpecHelper.html#getQueue()"><B>getQueue()</B></A> - \r
1067 Method in class compbio.runner.<A HREF="../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner">_NativeSpecHelper</A>\r
1068 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
1069 <DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#getQueueByMemoryRequirements(int)"><B>getQueueByMemoryRequirements(int)</B></A> - \r
1070 Static method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
1071 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
1072 <DT><A HREF="../compbio/data/sequence/Score.html#getRanges()"><B>getRanges()</B></A> - \r
1073 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
1074 <DD>Return Ranges if any Collections.EMPTY_SET otherwise\r
1075 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getRawUsage()"><B>getRawUsage()</B></A> - \r
1076 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
1077 <DD>&nbsp;\r
1078 <DT><A HREF="../compbio/engine/local/LocalEngineUtil.html#getRecordedJobStatus(java.lang.String)"><B>getRecordedJobStatus(String)</B></A> - \r
1079 Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</A>\r
1080 <DD>&nbsp;\r
1081 <DT><A HREF="../compbio/ws/server/_WSLogger.html#getRemoteAddress()"><B>getRemoteAddress()</B></A> - \r
1082 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/_WSLogger.html" title="class in compbio.ws.server">_WSLogger</A>\r
1083 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
1084 <DT><A HREF="../compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws"><B>GetResult</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetResult.html#GetResult()"><B>GetResult()</B></A> - \r
1085 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResult.html" title="class in compbio.data.msa.jaxws">GetResult</A>\r
1086 <DD>&nbsp;\r
1087 <DT><A HREF="../compbio/data/msa/MsaWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
1088 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
1089 <DD>Return the result of the job.\r
1090 <DT><A HREF="../compbio/ws/server/_MsaService.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
1091 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/_MsaService.html" title="class in compbio.ws.server">_MsaService</A>\r
1092 <DD>&nbsp;\r
1093 <DT><A HREF="../compbio/ws/server/ClustalOWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
1094 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
1095 <DD>&nbsp;\r
1096 <DT><A HREF="../compbio/ws/server/ClustalWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
1097 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
1098 <DD>&nbsp;\r
1099 <DT><A HREF="../compbio/ws/server/MafftWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
1100 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
1101 <DD>&nbsp;\r
1102 <DT><A HREF="../compbio/ws/server/MuscleWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
1103 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
1104 <DD>&nbsp;\r
1105 <DT><A HREF="../compbio/ws/server/ProbconsWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
1106 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
1107 <DD>&nbsp;\r
1108 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
1109 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
1110 <DD>&nbsp;\r
1111 <DT><A HREF="../compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws"><B>GetResultResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetResultResponse.html#GetResultResponse()"><B>GetResultResponse()</B></A> - \r
1112 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws">GetResultResponse</A>\r
1113 <DD>&nbsp;\r
1114 <DT><A HREF="../compbio/engine/AsyncExecutor.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1115 Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>\r
1116 <DD>Retrieve the results of the job.\r
1117 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getResults()"><B>getResults()</B></A> - \r
1118 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
1119 <DD>&nbsp;\r
1120 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1121 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
1122 <DD>&nbsp;\r
1123 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getResults()"><B>getResults()</B></A> - \r
1124 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
1125 <DD>&nbsp;\r
1126 <DT><A HREF="../compbio/engine/client/Executable.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1127 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>\r
1128 <DD>&nbsp;\r
1129 <DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1130 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>\r
1131 <DD>&nbsp;\r
1132 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1133 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
1134 <DD>&nbsp;\r
1135 <DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1136 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
1137 <DD>&nbsp;\r
1138 <DT><A HREF="../compbio/engine/local/LocalEngineUtil.html#getResults(java.util.concurrent.Future, java.lang.String)"><B>getResults(Future&lt;ConfiguredExecutable&lt;?&gt;&gt;, String)</B></A> - \r
1139 Static method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalEngineUtil.html" title="class in compbio.engine.local">LocalEngineUtil</A>\r
1140 <DD>&nbsp;\r
1141 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1142 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
1143 <DD>&nbsp;\r
1144 <DT><A HREF="../compbio/runner/_SkeletalCommandBuilder.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1145 Method in class compbio.runner.<A HREF="../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>\r
1146 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
1147 <DT><A HREF="../compbio/runner/conservation/AACon.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1148 Method in class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>\r
1149 <DD>&nbsp;\r
1150 <DT><A HREF="../compbio/runner/disorder/Disembl.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1151 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>\r
1152 <DD>&nbsp;\r
1153 <DT><A HREF="../compbio/runner/disorder/GlobPlot.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1154 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>\r
1155 <DD>&nbsp;\r
1156 <DT><A HREF="../compbio/runner/disorder/IUPred.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1157 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>\r
1158 <DD>&nbsp;\r
1159 <DT><A HREF="../compbio/runner/disorder/Jronn.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1160 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>\r
1161 <DD>&nbsp;\r
1162 <DT><A HREF="../compbio/runner/msa/ClustalO.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1163 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>\r
1164 <DD>&nbsp;\r
1165 <DT><A HREF="../compbio/runner/msa/ClustalW.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1166 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
1167 <DD>&nbsp;\r
1168 <DT><A HREF="../compbio/runner/msa/Mafft.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1169 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>\r
1170 <DD>&nbsp;\r
1171 <DT><A HREF="../compbio/runner/msa/Muscle.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1172 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
1173 <DD>&nbsp;\r
1174 <DT><A HREF="../compbio/runner/msa/Probcons.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1175 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>\r
1176 <DD>&nbsp;\r
1177 <DT><A HREF="../compbio/runner/msa/Tcoffee.html#getResults(java.lang.String)"><B>getResults(String)</B></A> - \r
1178 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
1179 <DD>&nbsp;\r
1180 <DT><A HREF="../compbio/stat/collector/JobStat.html#getResultSize()"><B>getResultSize()</B></A> - \r
1181 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
1182 <DD>&nbsp;\r
1183 <DT><A HREF="../compbio/data/msa/jaxws/AlignResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1184 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws">AlignResponse</A>\r
1185 <DD>&nbsp;\r
1186 <DT><A HREF="../compbio/data/msa/jaxws/AnalizeResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1187 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AnalizeResponse.html" title="class in compbio.data.msa.jaxws">AnalizeResponse</A>\r
1188 <DD>&nbsp;\r
1189 <DT><A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1190 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAlignResponse.html" title="class in compbio.data.msa.jaxws">CustomAlignResponse</A>\r
1191 <DD>&nbsp;\r
1192 <DT><A HREF="../compbio/data/msa/jaxws/CustomAnalizeResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1193 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/CustomAnalizeResponse.html" title="class in compbio.data.msa.jaxws">CustomAnalizeResponse</A>\r
1194 <DD>&nbsp;\r
1195 <DT><A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1196 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetAnnotationResponse.html" title="class in compbio.data.msa.jaxws">GetAnnotationResponse</A>\r
1197 <DD>&nbsp;\r
1198 <DT><A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1199 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetJobStatusResponse.html" title="class in compbio.data.msa.jaxws">GetJobStatusResponse</A>\r
1200 <DD>&nbsp;\r
1201 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1202 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedOnResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedOnResponse</A>\r
1203 <DD>&nbsp;\r
1204 <DT><A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1205 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLastTestedResponse.html" title="class in compbio.data.msa.jaxws">GetLastTestedResponse</A>\r
1206 <DD>&nbsp;\r
1207 <DT><A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1208 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitResponse.html" title="class in compbio.data.msa.jaxws">GetLimitResponse</A>\r
1209 <DD>&nbsp;\r
1210 <DT><A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1211 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetLimitsResponse.html" title="class in compbio.data.msa.jaxws">GetLimitsResponse</A>\r
1212 <DD>&nbsp;\r
1213 <DT><A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1214 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetPresetsResponse.html" title="class in compbio.data.msa.jaxws">GetPresetsResponse</A>\r
1215 <DD>&nbsp;\r
1216 <DT><A HREF="../compbio/data/msa/jaxws/GetResultResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1217 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetResultResponse.html" title="class in compbio.data.msa.jaxws">GetResultResponse</A>\r
1218 <DD>&nbsp;\r
1219 <DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1220 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws">GetRunnerOptionsResponse</A>\r
1221 <DD>&nbsp;\r
1222 <DT><A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1223 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html" title="class in compbio.data.msa.jaxws">GetSupportedServicesResponse</A>\r
1224 <DD>&nbsp;\r
1225 <DT><A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1226 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAlignResponse.html" title="class in compbio.data.msa.jaxws">PresetAlignResponse</A>\r
1227 <DD>&nbsp;\r
1228 <DT><A HREF="../compbio/data/msa/jaxws/PresetAnalizeResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1229 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PresetAnalizeResponse.html" title="class in compbio.data.msa.jaxws">PresetAnalizeResponse</A>\r
1230 <DD>&nbsp;\r
1231 <DT><A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1232 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/PullExecStatisticsResponse.html" title="class in compbio.data.msa.jaxws">PullExecStatisticsResponse</A>\r
1233 <DD>&nbsp;\r
1234 <DT><A HREF="../compbio/data/msa/jaxws/TestAllServicesResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1235 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestAllServicesResponse.html" title="class in compbio.data.msa.jaxws">TestAllServicesResponse</A>\r
1236 <DD>&nbsp;\r
1237 <DT><A HREF="../compbio/data/msa/jaxws/TestServiceResponse.html#getReturn()"><B>getReturn()</B></A> - \r
1238 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/TestServiceResponse.html" title="class in compbio.data.msa.jaxws">TestServiceResponse</A>\r
1239 <DD>&nbsp;\r
1240 <DT><A HREF="../compbio/runner/_impl/Runners.html#getRonnRunnable(java.lang.String)"><B>getRonnRunnable(String)</B></A> - \r
1241 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
1242 <DD>&nbsp;\r
1243 <DT><A HREF="../compbio/runner/_impl/Environment.html#getRPSBlastDatabasesDir()"><B>getRPSBlastDatabasesDir()</B></A> - \r
1244 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Environment.html" title="class in compbio.runner._impl">Environment</A>\r
1245 <DD>&nbsp;\r
1246 <DT><A HREF="../compbio/runner/_impl/Runners.html#getRPSBlastRunnable(java.lang.String)"><B>getRPSBlastRunnable(String)</B></A> - \r
1247 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
1248 <DD>&nbsp;\r
1249 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getRunConfiguration()"><B>getRunConfiguration()</B></A> - \r
1250 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
1251 <DD>&nbsp;\r
1252 <DT><A HREF="../compbio/ws/client/ServicesUtil.html#getRunnerByJobDirectory(java.io.File)"><B>getRunnerByJobDirectory(File)</B></A> - \r
1253 Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</A>\r
1254 <DD>&nbsp;\r
1255 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#getRunnerClassName()"><B>getRunnerClassName()</B></A> - \r
1256 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
1257 <DD>&nbsp;\r
1258 <DT><A HREF="../compbio/metadata/PresetManager.html#getRunnerClassName()"><B>getRunnerClassName()</B></A> - \r
1259 Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
1260 <DD>&nbsp;\r
1261 <DT><A HREF="../compbio/metadata/RunnerConfig.html#getRunnerClassName()"><B>getRunnerClassName()</B></A> - \r
1262 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
1263 <DD>&nbsp;\r
1264 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getRunnerLimits(java.lang.Class)"><B>getRunnerLimits(Class&lt;V&gt;)</B></A> - \r
1265 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
1266 <DD>This method should be executed once and result of its execution reused.\r
1267 <DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptions.html" title="class in compbio.data.msa.jaxws"><B>GetRunnerOptions</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptions.html#GetRunnerOptions()"><B>GetRunnerOptions()</B></A> - \r
1268 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetRunnerOptions.html" title="class in compbio.data.msa.jaxws">GetRunnerOptions</A>\r
1269 <DD>&nbsp;\r
1270 <DT><A HREF="../compbio/data/msa/Metadata.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
1271 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A>\r
1272 <DD>Get options supported by a web service\r
1273 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getRunnerOptions(java.lang.Class)"><B>getRunnerOptions(Class&lt;? extends Executable&lt;V&gt;&gt;)</B></A> - \r
1274 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
1275 <DD>&nbsp;\r
1276 <DT><A HREF="../compbio/ws/server/ClustalOWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
1277 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>\r
1278 <DD>&nbsp;\r
1279 <DT><A HREF="../compbio/ws/server/ClustalWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
1280 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>\r
1281 <DD>&nbsp;\r
1282 <DT><A HREF="../compbio/ws/server/GenericMetadataService.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
1283 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/GenericMetadataService.html" title="class in compbio.ws.server">GenericMetadataService</A>\r
1284 <DD>&nbsp;\r
1285 <DT><A HREF="../compbio/ws/server/MafftWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
1286 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>\r
1287 <DD>&nbsp;\r
1288 <DT><A HREF="../compbio/ws/server/MuscleWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
1289 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>\r
1290 <DD>&nbsp;\r
1291 <DT><A HREF="../compbio/ws/server/ProbconsWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
1292 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>\r
1293 <DD>&nbsp;\r
1294 <DT><A HREF="../compbio/ws/server/TcoffeeWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
1295 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A>\r
1296 <DD>&nbsp;\r
1297 <DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws"><B>GetRunnerOptionsResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#GetRunnerOptionsResponse()"><B>GetRunnerOptionsResponse()</B></A> - \r
1298 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html" title="class in compbio.data.msa.jaxws">GetRunnerOptionsResponse</A>\r
1299 <DD>&nbsp;\r
1300 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getRunnerPresets(java.lang.Class)"><B>getRunnerPresets(Class&lt;? extends Executable&lt;V&gt;&gt;)</B></A> - \r
1301 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
1302 <DD>&nbsp;\r
1303 <DT><A HREF="../compbio/stat/collector/JobStat.html#getRuntime()"><B>getRuntime()</B></A> - \r
1304 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
1305 <DD>&nbsp;\r
1306 <DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#getSchema(java.lang.String)"><B>getSchema(String)</B></A> - \r
1307 Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
1308 <DD>&nbsp;\r
1309 <DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#getScoreByMethod(java.lang.Enum)"><B>getScoreByMethod(Enum&lt;?&gt;)</B></A> - \r
1310 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>\r
1311 <DD>&nbsp;\r
1312 <DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#getScoreByMethod(java.lang.String)"><B>getScoreByMethod(String)</B></A> - \r
1313 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>\r
1314 <DD>&nbsp;\r
1315 <DT><A HREF="../compbio/data/sequence/Score.html#getScores()"><B>getScores()</B></A> - \r
1316 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
1317 <DD>The column scores for the alignment\r
1318 <DT><A HREF="../compbio/metadata/Limit.html#getSeqNumber()"><B>getSeqNumber()</B></A> - \r
1319 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
1320 <DD>&nbsp;\r
1321 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#getSequence()"><B>getSequence()</B></A> - \r
1322 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
1323 <DD>Gets the value of sequence\r
1324 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getSequenceLenghtActual()"><B>getSequenceLenghtActual()</B></A> - \r
1325 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
1326 <DD>&nbsp;\r
1327 <DT><A HREF="../compbio/metadata/LimitExceededException.html#getSequenceLenghtActual()"><B>getSequenceLenghtActual()</B></A> - \r
1328 Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
1329 <DD>&nbsp;\r
1330 <DT><A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html#getSequenceLenghtAllowed()"><B>getSequenceLenghtAllowed()</B></A> - \r
1331 Method in class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/LimitExceededExceptionBean.html" title="class in compbio.data.msa.jaxws">LimitExceededExceptionBean</A>\r
1332 <DD>&nbsp;\r
1333 <DT><A HREF="../compbio/metadata/LimitExceededException.html#getSequenceLenghtAllowed()"><B>getSequenceLenghtAllowed()</B></A> - \r
1334 Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
1335 <DD>&nbsp;\r
1336 <DT><A HREF="../compbio/data/sequence/Alignment.html#getSequences()"><B>getSequences()</B></A> - \r
1337 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
1338 <DD>&nbsp;\r
1339 <DT><A HREF="../compbio/ws/client/Services.html#getService(java.lang.String)"><B>getService(String)</B></A> - \r
1340 Static method in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>\r
1341 <DD>&nbsp;\r
1342 <DT><A HREF="../compbio/ws/client/ServicesUtil.html#getServiceByJobDirectory(java.io.File)"><B>getServiceByJobDirectory(File)</B></A> - \r
1343 Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</A>\r
1344 <DD>&nbsp;\r
1345 <DT><A HREF="../compbio/ws/client/ServicesUtil.html#getServiceByRunner(java.lang.Class)"><B>getServiceByRunner(Class&lt;Executable&lt;?&gt;&gt;)</B></A> - \r
1346 Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</A>\r
1347 <DD>&nbsp;\r
1348 <DT><A HREF="../compbio/ws/client/ServicesUtil.html#getServiceImpl(compbio.ws.client.Services)"><B>getServiceImpl(Services)</B></A> - \r
1349 Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/ServicesUtil.html" title="class in compbio.ws.client">ServicesUtil</A>\r
1350 <DD>&nbsp;\r
1351 <DT><A HREF="../compbio/ws/client/Jws2Client.html#getServices(java.lang.String)"><B>getServices(String)</B></A> - \r
1352 Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
1353 <DD>&nbsp;\r
1354 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#getSession()"><B>getSession()</B></A> - \r
1355 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
1356 <DD>&nbsp;\r
1357 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#getSingleWSStat(compbio.ws.client.Services)"><B>getSingleWSStat(Services)</B></A> - \r
1358 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
1359 <DD>&nbsp;\r
1360 <DT><A HREF="../compbio/data/sequence/Alignment.html#getSize()"><B>getSize()</B></A> - \r
1361 Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
1362 <DD>&nbsp;\r
1363 <DT><A HREF="../compbio/data/sequence/SMERFSConstraints.html#getSMERFSColumnScore(java.lang.String)"><B>getSMERFSColumnScore(String)</B></A> - \r
1364 Static method in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A>\r
1365 <DD>&nbsp;\r
1366 <DT><A HREF="../compbio/stat/collector/JobStat.html#getStart()"><B>getStart()</B></A> - \r
1367 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
1368 <DD>&nbsp;\r
1369 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getStartTime()"><B>getStartTime()</B></A> - \r
1370 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
1371 <DD>&nbsp;\r
1372 <DT><A HREF="../compbio/runner/conservation/AACon.html#getStatFile()"><B>getStatFile()</B></A> - \r
1373 Static method in class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>\r
1374 <DD>&nbsp;\r
1375 <DT><A HREF="../compbio/runner/disorder/Jronn.html#getStatFile()"><B>getStatFile()</B></A> - \r
1376 Static method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>\r
1377 <DD>&nbsp;\r
1378 <DT><A HREF="../compbio/runner/msa/ClustalO.html#getStatFile()"><B>getStatFile()</B></A> - \r
1379 Static method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>\r
1380 <DD>&nbsp;\r
1381 <DT><A HREF="../compbio/runner/msa/ClustalW.html#getStatFile()"><B>getStatFile()</B></A> - \r
1382 Static method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
1383 <DD>&nbsp;\r
1384 <DT><A HREF="../compbio/runner/msa/Muscle.html#getStatFile()"><B>getStatFile()</B></A> - \r
1385 Static method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
1386 <DD>&nbsp;\r
1387 <DT><A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html#getStatistics(org.ggf.drmaa.JobInfo)"><B>getStatistics(JobInfo)</B></A> - \r
1388 Static method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/ClusterSession.html" title="class in compbio.engine.cluster.drmaa">ClusterSession</A>\r
1389 <DD>&nbsp;\r
1390 <DT><A HREF="../compbio/ws/server/_WSLogger.html#getStatLogger(compbio.ws.client.Services, javax.xml.ws.WebServiceContext)"><B>getStatLogger(Services, WebServiceContext)</B></A> - \r
1391 Static method in class compbio.ws.server.<A HREF="../compbio/ws/server/_WSLogger.html" title="class in compbio.ws.server">_WSLogger</A>\r
1392 <DD><B>Deprecated.</B>&nbsp;&nbsp;\r
1393 <DT><A HREF="../compbio/stat/servlet/util/StatCollection.html#getStats(int)"><B>getStats(int)</B></A> - \r
1394 Static method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</A>\r
1395 <DD>&nbsp;\r
1396 <DT><A HREF="../compbio/stat/servlet/util/StatCollection.html#getStats(java.util.Date)"><B>getStats(Date)</B></A> - \r
1397 Static method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</A>\r
1398 <DD>&nbsp;\r
1399 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getSubmissionTime()"><B>getSubmissionTime()</B></A> - \r
1400 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
1401 <DD>&nbsp;\r
1402 <DT><A HREF="../compbio/runner/Util.html#getSupportedOptions(java.lang.Class)"><B>getSupportedOptions(Class&lt;? extends Executable&lt;T&gt;&gt;)</B></A> - \r
1403 Static method in class compbio.runner.<A HREF="../compbio/runner/Util.html" title="class in compbio.runner">Util</A>\r
1404 <DD>&nbsp;\r
1405 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getSupportedRuntimes()"><B>getSupportedRuntimes()</B></A> - \r
1406 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
1407 <DD>&nbsp;\r
1408 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getSupportedRuntimes()"><B>getSupportedRuntimes()</B></A> - \r
1409 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
1410 <DD>&nbsp;\r
1411 <DT><A HREF="../compbio/engine/client/Util.html#getSupportedRuntimes(java.lang.Class)"><B>getSupportedRuntimes(Class&lt;?&gt;)</B></A> - \r
1412 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
1413 <DD>&nbsp;\r
1414 <DT><A HREF="../compbio/data/msa/jaxws/GetSupportedServices.html" title="class in compbio.data.msa.jaxws"><B>GetSupportedServices</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetSupportedServices.html#GetSupportedServices()"><B>GetSupportedServices()</B></A> - \r
1415 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetSupportedServices.html" title="class in compbio.data.msa.jaxws">GetSupportedServices</A>\r
1416 <DD>&nbsp;\r
1417 <DT><A HREF="../compbio/data/msa/RegistryWS.html#getSupportedServices()"><B>getSupportedServices()</B></A> - \r
1418 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa">RegistryWS</A>\r
1419 <DD>List of services that are functioning on the server.\r
1420 <DT><A HREF="../compbio/ws/server/RegistryWS.html#getSupportedServices()"><B>getSupportedServices()</B></A> - \r
1421 Method in class compbio.ws.server.<A HREF="../compbio/ws/server/RegistryWS.html" title="class in compbio.ws.server">RegistryWS</A>\r
1422 <DD>&nbsp;\r
1423 <DT><A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html" title="class in compbio.data.msa.jaxws"><B>GetSupportedServicesResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html#GetSupportedServicesResponse()"><B>GetSupportedServicesResponse()</B></A> - \r
1424 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/GetSupportedServicesResponse.html" title="class in compbio.data.msa.jaxws">GetSupportedServicesResponse</A>\r
1425 <DD>&nbsp;\r
1426 <DT><A HREF="../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)"><B>getSyncEngine(ConfiguredExecutable&lt;?&gt;, Executable.ExecProvider)</B></A> - \r
1427 Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
1428 <DD>&nbsp;\r
1429 <DT><A HREF="../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable)"><B>getSyncEngine(ConfiguredExecutable&lt;?&gt;)</B></A> - \r
1430 Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
1431 <DD>&nbsp;\r
1432 <DT><A HREF="../compbio/engine/SubmissionManager.html#getTask(java.lang.String)"><B>getTask(String)</B></A> - \r
1433 Static method in class compbio.engine.<A HREF="../compbio/engine/SubmissionManager.html" title="class in compbio.engine">SubmissionManager</A>\r
1434 <DD>&nbsp;\r
1435 <DT><A HREF="../compbio/engine/conf/DirectoryManager.html#getTaskDirectory(java.lang.Class)"><B>getTaskDirectory(Class&lt;?&gt;)</B></A> - \r
1436 Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/DirectoryManager.html" title="class in compbio.engine.conf">DirectoryManager</A>\r
1437 <DD>&nbsp;\r
1438 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getTaskId()"><B>getTaskId()</B></A> - \r
1439 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
1440 <DD>&nbsp;\r
1441 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getTaskId()"><B>getTaskId()</B></A> - \r
1442 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
1443 <DD>&nbsp;\r
1444 <DT><A HREF="../compbio/engine/Job.html#getTaskId()"><B>getTaskId()</B></A> - \r
1445 Method in class compbio.engine.<A HREF="../compbio/engine/Job.html" title="class in compbio.engine">Job</A>\r
1446 <DD>&nbsp;\r
1447 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getTestArgs()"><B>getTestArgs()</B></A> - \r
1448 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
1449 <DD>&nbsp;\r
1450 <DT><A HREF="../compbio/runner/_impl/OB.html#getTestArgs()"><B>getTestArgs()</B></A> - \r
1451 Method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>\r
1452 <DD>&nbsp;\r
1453 <DT><A HREF="../compbio/runner/_impl/Mcl.html#getTestCommand()"><B>getTestCommand()</B></A> - \r
1454 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
1455 <DD>&nbsp;\r
1456 <DT><A HREF="../compbio/runner/_impl/NetNglyc.html#getTestCommand()"><B>getTestCommand()</B></A> - \r
1457 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
1458 <DD>&nbsp;\r
1459 <DT><A HREF="../compbio/runner/_impl/OB.html#getTestCommand()"><B>getTestCommand()</B></A> - \r
1460 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>\r
1461 <DD>&nbsp;\r
1462 <DT><A HREF="../compbio/runner/_impl/Ronn.html#getTestCommand()"><B>getTestCommand()</B></A> - \r
1463 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>\r
1464 <DD>&nbsp;\r
1465 <DT><A HREF="../compbio/runner/_impl/RPSBlast.html#getTestCommand()"><B>getTestCommand()</B></A> - \r
1466 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A>\r
1467 <DD>&nbsp;\r
1468 <DT><A HREF="../compbio/runner/_impl/Mcl.html#getTestParams()"><B>getTestParams()</B></A> - \r
1469 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>\r
1470 <DD>&nbsp;\r
1471 <DT><A HREF="../compbio/engine/cluster/dundee/_Queue.html#getTimeLimit()"><B>getTimeLimit()</B></A> - \r
1472 Method in enum compbio.engine.cluster.dundee.<A HREF="../compbio/engine/cluster/dundee/_Queue.html" title="enum in compbio.engine.cluster.dundee">_Queue</A>\r
1473 <DD><B>Deprecated.</B>&nbsp;0 - unlimited\r
1474 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getTimeStat()"><B>getTimeStat()</B></A> - \r
1475 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
1476 <DD>&nbsp;\r
1477 <DT><A HREF="../compbio/runner/_impl/Runners.html#getTmhmm2Runnable(java.lang.String)"><B>getTmhmm2Runnable(String)</B></A> - \r
1478 Static method in class compbio.runner._impl.<A HREF="../compbio/runner/_impl/Runners.html" title="class in compbio.runner._impl">Runners</A>\r
1479 <DD>&nbsp;\r
1480 <DT><A HREF="../compbio/stat/servlet/util/Totals.html#getTotal()"><B>getTotal()</B></A> - \r
1481 Method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/Totals.html" title="class in compbio.stat.servlet.util">Totals</A>\r
1482 <DD>&nbsp;\r
1483 <DT><A HREF="../compbio/stat/collector/StatDB.html#getTotalJobsCount(java.sql.Timestamp, java.sql.Timestamp)"><B>getTotalJobsCount(Timestamp, Timestamp)</B></A> - \r
1484 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</A>\r
1485 <DD>&nbsp;\r
1486 <DT><A HREF="../compbio/stat/collector/StatProcessor.html#getTotalRuntime()"><B>getTotalRuntime()</B></A> - \r
1487 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/StatProcessor.html" title="class in compbio.stat.collector">StatProcessor</A>\r
1488 <DD>&nbsp;\r
1489 <DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#getType()"><B>getType()</B></A> - \r
1490 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
1491 <DD>&nbsp;\r
1492 <DT><A HREF="../compbio/metadata/ValueConstrain.html#getType()"><B>getType()</B></A> - \r
1493 Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
1494 <DD>&nbsp;\r
1495 <DT><A HREF="../compbio/runner/conservation/AACon.html#getType()"><B>getType()</B></A> - \r
1496 Method in class compbio.runner.conservation.<A HREF="../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>\r
1497 <DD>&nbsp;\r
1498 <DT><A HREF="../compbio/runner/disorder/Disembl.html#getType()"><B>getType()</B></A> - \r
1499 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>\r
1500 <DD>&nbsp;\r
1501 <DT><A HREF="../compbio/runner/disorder/GlobPlot.html#getType()"><B>getType()</B></A> - \r
1502 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>\r
1503 <DD>&nbsp;\r
1504 <DT><A HREF="../compbio/runner/disorder/IUPred.html#getType()"><B>getType()</B></A> - \r
1505 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>\r
1506 <DD>&nbsp;\r
1507 <DT><A HREF="../compbio/runner/disorder/Jronn.html#getType()"><B>getType()</B></A> - \r
1508 Method in class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>\r
1509 <DD>&nbsp;\r
1510 <DT><A HREF="../compbio/runner/msa/ClustalO.html#getType()"><B>getType()</B></A> - \r
1511 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>\r
1512 <DD>&nbsp;\r
1513 <DT><A HREF="../compbio/runner/msa/ClustalW.html#getType()"><B>getType()</B></A> - \r
1514 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>\r
1515 <DD>&nbsp;\r
1516 <DT><A HREF="../compbio/runner/msa/Mafft.html#getType()"><B>getType()</B></A> - \r
1517 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>\r
1518 <DD>&nbsp;\r
1519 <DT><A HREF="../compbio/runner/msa/Muscle.html#getType()"><B>getType()</B></A> - \r
1520 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>\r
1521 <DD>&nbsp;\r
1522 <DT><A HREF="../compbio/runner/msa/Probcons.html#getType()"><B>getType()</B></A> - \r
1523 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>\r
1524 <DD>&nbsp;\r
1525 <DT><A HREF="../compbio/runner/msa/Tcoffee.html#getType()"><B>getType()</B></A> - \r
1526 Method in class compbio.runner.msa.<A HREF="../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>\r
1527 <DD>&nbsp;\r
1528 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getUsedSysTime()"><B>getUsedSysTime()</B></A> - \r
1529 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
1530 <DD>&nbsp;\r
1531 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getUsedUserTime()"><B>getUsedUserTime()</B></A> - \r
1532 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
1533 <DD>&nbsp;\r
1534 <DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#getValidator(java.lang.String)"><B>getValidator(String)</B></A> - \r
1535 Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
1536 <DD>&nbsp;\r
1537 <DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#getValidator(javax.xml.validation.Schema)"><B>getValidator(Schema)</B></A> - \r
1538 Static method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
1539 <DD>&nbsp;\r
1540 <DT><A HREF="../compbio/metadata/Parameter.html#getValidValue()"><B>getValidValue()</B></A> - \r
1541 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
1542 <DD>&nbsp;\r
1543 <DT><A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html#getVMem()"><B>getVMem()</B></A> - \r
1544 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/StatisticManager.html" title="class in compbio.engine.cluster.drmaa">StatisticManager</A>\r
1545 <DD>&nbsp;\r
1546 <DT><A HREF="../compbio/stat/collector/JobStat.html#getWebService()"><B>getWebService()</B></A> - \r
1547 Method in class compbio.stat.collector.<A HREF="../compbio/stat/collector/JobStat.html" title="class in compbio.stat.collector">JobStat</A>\r
1548 <DD>&nbsp;\r
1549 <DT><A HREF="../compbio/engine/AsyncExecutor.html#getWorkDirectory(java.lang.String)"><B>getWorkDirectory(String)</B></A> - \r
1550 Method in interface compbio.engine.<A HREF="../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A>\r
1551 <DD>&nbsp;\r
1552 <DT><A HREF="../compbio/engine/client/ConfExecutable.html#getWorkDirectory()"><B>getWorkDirectory()</B></A> - \r
1553 Method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
1554 <DD>&nbsp;\r
1555 <DT><A HREF="../compbio/engine/client/ConfiguredExecutable.html#getWorkDirectory()"><B>getWorkDirectory()</B></A> - \r
1556 Method in interface compbio.engine.client.<A HREF="../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>\r
1557 <DD>&nbsp;\r
1558 <DT><A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getWorkDirectory(java.lang.String)"><B>getWorkDirectory(String)</B></A> - \r
1559 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/AsyncJobRunner.html" title="class in compbio.engine.cluster.drmaa">AsyncJobRunner</A>\r
1560 <DD>&nbsp;\r
1561 <DT><A HREF="../compbio/engine/cluster/drmaa/JobRunner.html#getWorkDirectory()"><B>getWorkDirectory()</B></A> - \r
1562 Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>\r
1563 <DD>&nbsp;\r
1564 <DT><A HREF="../compbio/engine/Configurator.html#getWorkDirectory(java.lang.String)"><B>getWorkDirectory(String)</B></A> - \r
1565 Static method in class compbio.engine.<A HREF="../compbio/engine/Configurator.html" title="class in compbio.engine">Configurator</A>\r
1566 <DD>&nbsp;\r
1567 <DT><A HREF="../compbio/engine/local/AsyncLocalRunner.html#getWorkDirectory(java.lang.String)"><B>getWorkDirectory(String)</B></A> - \r
1568 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/AsyncLocalRunner.html" title="class in compbio.engine.local">AsyncLocalRunner</A>\r
1569 <DD>&nbsp;\r
1570 <DT><A HREF="../compbio/engine/local/LocalRunner.html#getWorkDirectory()"><B>getWorkDirectory()</B></A> - \r
1571 Method in class compbio.engine.local.<A HREF="../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A>\r
1572 <DD>&nbsp;\r
1573 <DT><A HREF="../compbio/engine/SyncExecutor.html#getWorkDirectory()"><B>getWorkDirectory()</B></A> - \r
1574 Method in interface compbio.engine.<A HREF="../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A>\r
1575 <DD>&nbsp;\r
1576 <DT><A HREF="../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder"><B>GlobPlot</B></A> - Class in <A HREF="../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A><DD>./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame
1577
1578  FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file'
1579  Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file'
1580
1581  Hard-coded values are 10 15 74 4 5.<DT><A HREF="../compbio/runner/disorder/GlobPlot.html#GlobPlot()"><B>GlobPlot()</B></A> - \r
1582 Constructor for class compbio.runner.disorder.<A HREF="../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>\r
1583 <DD>&nbsp;\r
1584 <DT><A HREF="../compbio/ws/server/GlobPlotWS.html" title="class in compbio.ws.server"><B>GlobPlotWS</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/GlobPlotWS.html#GlobPlotWS()"><B>GlobPlotWS()</B></A> - \r
1585 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/GlobPlotWS.html" title="class in compbio.ws.server">GlobPlotWS</A>\r
1586 <DD>&nbsp;\r
1587 </DL>\r
1588 <HR>\r
1589 \r
1590 \r
1591 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
1592 <A NAME="navbar_bottom"><!-- --></A>\r
1593 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
1594 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
1595 <TR>\r
1596 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
1597 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
1598 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
1599   <TR ALIGN="center" VALIGN="top">\r
1600   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
1601   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
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1603   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
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1605   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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1607   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
1608   </TR>\r
1609 </TABLE>\r
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1611 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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1616 <TR>\r
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1620 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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1626     document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
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